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Okeydokey. I found a bug where the Queen could climb if a game was saved while the Throne Room was "popped" on mouse over, and then that game was loaded with the mouse cursor not being over the Throne Room, resulting in the Queen being spawned at her higher "popped" position. I also found a possible bug where switching between inspect mode while having the mouse over/not over the Queen and Throne Room in certain combinations (combinations more likely when the camera is tilted) could also result in some oddness.

I've got fixes for both of these, and something to check for bad saved Queen positions that will go out in the next patch. Unless something more specific rears its head, I'm happy to assume for now that these will address what you've experienced.